Gene of interest

Introduction to Bioconductor in R

Paula Andrea Martinez, PhD.

Data Scientist

Examples of genomic intervals

Reads aligned to a reference
Genes of interest
Exonic regions
Single nucleotide polymorphisms (SNPs)
Regions of transcription or binding sites, RNA-seq or ChIP-seq

Genomic Ranges

library(GenomicRanges)
(myGR <- GRanges("chr1:200-300"))

 GRanges object with 1 range and 0 metadata columns:
  seqnames     ranges strand
     <Rle>  <IRanges>  <Rle>
[1]     chr1 [200, 300]    *
 -----
seqinfo: 1 sequence from an unspecified genome; no seqlengths

GRanges class is a container to save genomic intervals by chromosome
Minimum arguments chr1:200-300
GRanges seqnames and seqinfo

# df a data.frame like structure
   seqnames start end strand score  GC
1     chrX    50 120      +     1 0.25 
2     chrX   130 140      +     2 0.25 
3     chrX   153 154      +     3 0.25 
4     chrY    30  40      *     4 0.25 
5     chrY    50  55      -     5 0.25

(myGR <- as(df, "GRanges")) # transform df into GRanges

GRanges object with 5 ranges and 2 metadata columns:
      seqnames     ranges strand |     score        GC     
         <Rle>  <IRanges>  <Rle> | <integer> <numeric>
  [1]     chrX [ 50, 120]      + |         1      0.25   
  [2]     chrX [130, 140]      + |         2      0.25   
  [3]     chrX [153, 154]      + |         3      0.25   
  [4]     chrY [ 30,  40]      * |         4      0.25   
  [5]     chrY [ 50,  55]      - |         5      0.25   
 -----
 seqinfo: 2 sequences from an unspecified genome; no seqlengths

Genomic Ranges accessors

methods(class = "GRanges") # to check available accessors

# used for chromosome names 
seqnames(gr)

# returns an IRanges object for ranges
ranges(gr)

# stores metadata columns
mcols(gr)

# generic function to store sequence information
seqinfo(gr)

# stores the genome name
genome(gr)

Accessors are both setter and getter functions
Accessors can be inherited thanks to S4 definitions

Gene of interest: ABCD1

ABCD1 is located at the end of chromosome X long arm
encodes a protein relevant for the well functioning of brain and lung cells in mammals
chrX is ~ 156 mi bp
Located chrX ~ 153.70 mi bp

https://www.ncbi.nlm.nih.gov/gene/215

ChrX-ABCD1

Chromosome X GRanges

library(TxDb.Hsapiens.UCSC.hg38.knownGene)
hg <- TxDb.Hsapiens.UCSC.hg38.knownGene

Select genes from chromosome X

hg_chrXg <- genes(hg, filter = list(tx_chrom = c("chrX")))

GRanges object with 1192 ranges and 1 metadata column:
            seqnames              ranges strand |     gene_id
               <Rle>           <IRanges>  <Rle> | <character>
  100008586     chrX   49551278-49568218      + |   100008586
      10009     chrX 120250752-120258398      + |       10009
  100093698     chrX   13310652-13319933      + |   100093698
        ...      ...                 ...    ... .         ...
  -------
  seqinfo: 640 sequences (1 circular) from hg38 genome

Let's practice looking for a gene of interest in the human genome!

Introduction to Bioconductor in R